Answers:
1. No sanctions yet if there is no stamp on your passport.
2. Maybe by using a new passport
3. Your current passport can go to other countries but maybe into Malaysia may be a problem. Depends a lot of which entry point.

Actually I entered Malaysia by airplane and I passed the Malaysian Immigration. When I was in Malaysia for 30 days, I personally applied for a 15-day extension. After that I was not allowed to apply for a visa. Then after 10 months of stayed in Sabah, I decided to go back home and I exited using speed boat to Tawi-Tawi.